Bibliography

Braun & Gõ, 1985

Braun, W. & Gõ, N. (1985).
J. Mol. Biol. 186, 611-626.

Brünger, 1992

Brünger, A. T. (1992).
X-PLOR Manual Version 3.1.
Yale University New Haven, Connecticut.

Felsenstein, 1985

Felsenstein, J. (1985).
Evolution, 39, 783-791.

Fiser et al., 2000

Fiser, A., Do, R. K. G., & Šali, A. (2000).
Protein Sci. 9, 1-21.
(Also available online).

Gotoh, 1982

Gotoh, O. (1982).
J. Mol. Biol. 162, 705-708.

Hubbard & Blundell, 1987

Hubbard, T. J. P. & Blundell, T. L. (1987).
Protein Eng. 1, 159-171.

IUPAC-IUB, 1970

IUPAC-IUB (1970).
Biochem. 9, 3471-3479.

Kabsch & Sander, 1983

Kabsch, W. & Sander, C. (1983).
Biopolymers, 22, 2577-2637.

Karlin & Altschul, 1990

Karlin, S. & Altschul, S. F. (1990).
Proc. Natl. Acad. Sci. USA, 87, 2264-2268.

Kendrew et al., 1970

Kendrew, J. C., Klyne, W., Lifson, S., Miyazawa, T., Némethy, G., Phillips, D. C., Ramachandran, G. N., & Scheraga, H. (1970).
J. Mol. Biol. 52, 1-17.

MacKerell et al., 1998

MacKerell, Jr., A. D., Bashford, D., Bellott, M., Dunbrack Jr., R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, III, W. E., Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., & Karplus, M. (1998).
J. Phys. Chem. B, 102, 3586-3616.

Martí-Renom et al., 2004

Martí-Renom, M. A., Madhusudhan, M. S., & Šali, A. (2004).
Protein Sci. 13, 1071-1087.
(Also available online).

Melo & Feytmans, 1997

Melo, F. & Feytmans, E. (1997).
J. Mol. Biol. 267, 207-222.

Melo et al., 2002

Melo, F., Sánchez, R., & Šali, A. (2002).
Protein Sci. 11, 430-448.
(Also available online).

Metropolis et al., 1953

Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H., & Teller, E. (1953).
J. Chem. Phys. 21, 1087-1092.

Needleman & Wunsch, 1970

Needleman, S. B. & Wunsch, C. D. (1970).
J. Mol. Biol. 48, 443-453.

Nicholls et al., 1991

Nicholls, A., Sharp, K. A., & Honig, B. (1991).
Proteins, 11, 281-296.

Press et al., 1992

Press, W. H., Teukolsky, S. A., Vetterling, W. T., & Flannery, B. P. (1992).
Numerical Recipes, 2nd edition.
Cambridge: Cambridge University Press.

Richards & Kundrot, 1988

Richards, F. M. & Kundrot, C. E. (1988).
Proteins, 3, 71-84.

Richmond & Richards, 1978

Richmond, T. J. & Richards, F. M. (1978).
J. Mol. Biol. 119, 537-555.

Šali & Blundell, 1990

Šali, A. & Blundell, T. L. (1990).
J. Mol. Biol. 212, 403-428.
(Also available online).

Šali & Blundell, 1993

Šali, A. & Blundell, T. L. (1993).
J. Mol. Biol. 234, 779-815.
(Also available online).

Šali & Overington, 1994

Šali, A. & Overington, J. (1994).
Protein Sci. 3, 1582-1596.
(Also available online).

Sankoff & Kruskal, 1983

Sankoff, D. & Kruskal, J. B. (1983).
Time warps, string edits, and macromolecules: The theory and practice of sequence comparison.
Reading, MA: Addison-Wesley Publishing Company.

Sellers, 1974

Sellers, P. H. (1974).
J. Comb. Theor. A16, 253-258.

Shanno & Phua, 1980

Shanno, D. F. & Phua, K. H. (1980).
ACM Trans. Math. Soft. 6, 618-622.

Shanno & Phua, 1982

Shanno, D. F. & Phua, K. H. (1982).
In: Collected algorithms from ACM. Trans. Math. Software volume 2(1).

Smith & Waterman, 1981

Smith, T. F. & Waterman, M. S. (1981).
J. Mol. Biol. 147, 195-197.

Subbiah et al., 1993

Subbiah, S., Laurents, D. V., & Levitt, M. (1993).
Curr. Biol. 3, 141-148.

Sutcliffe et al., 1987

Sutcliffe, M. J., Haneef, I., Carney, D., & Blundell, T. L. (1987).
Protein Eng. 1, 377-384.

Topf et al., 2005

Topf, M., Baker, M. L., John, B., Chiu, W., & Šali, A. (2005).
J. Struct. Biol. 149, 191-203.
(Also available online).

van Schaik et al., 1993

van Schaik, R. C., Berendsen, H. J., & Torda, A. E. (1993).
J. Mol. Biol. 234, 751-762.

Verlet, 1967

Verlet, J. (1967).
Phys. Rev. 159, 98-103.